test-coverage.yaml

on:
  push:
    branches:
      - main
      - master
  pull_request:
    branches:
      - main
      - master

name: test-coverage

jobs:
  test-coverage:
    runs-on: macOS-latest

    strategy:
      fail-fast: false
      matrix:
        config:
          - {os: macOS-latest,   r: 'release', bioc: '3.18'}

    env:
      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
    steps:
      - uses: actions/checkout@master

      - uses: r-lib/actions/setup-r@v2

      - uses: r-lib/actions/setup-pandoc@v2

      - uses: r-lib/actions/setup-tinytex@v2

      - run: tlmgr --version

      - name: Query dependencies
        run: |
          install.packages('remotes')
          saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2)
          message(paste('****', Sys.time(), 'installing BiocManager ****'))
          remotes::install_cran("BiocManager")
        shell: Rscript {0}

      ## Find the corresponding R version based on the Bioconductor version
      ## to use for the macOS and Windows checks by the next GHA job
      - id: findrversion
        name: Find Bioc and R versions
        run: |
          ## Find what branch we are working on
          if echo "$GITHUB_REF" | grep -q "master"; then
              biocversion="devel"
          elif echo "$GITHUB_REF" | grep -q "RELEASE_"; then
              biocversion="release"
          fi

          ## Define the R and Bioconductor version numbers
          biocversionnum=$(Rscript -e "info <- BiocManager:::.version_map_get_online('https://bioconductor.org/config.yaml'); res <- subset(info, BiocStatus == '${biocversion}')[, 'Bioc']; cat(as.character(res))")
          rversion=$(Rscript -e "info <- BiocManager:::.version_map_get_online('https://bioconductor.org/config.yaml'); res <- subset(info, BiocStatus == '${biocversion}')[, 'R']; cat(as.character(res))")

          ## Print the results
          echo $biocversion
          echo $biocversionnum
          echo $rversion

          ## Save the info for the next job
          echo "rversion=${rversion}" >> $GITHUB_OUTPUT
          echo "biocversionnum=${biocversionnum}" >> $GITHUB_OUTPUT
          # echo "::set-output name=rversion::${rversion}"
          # echo "::set-output name=biocversionnum::${biocversionnum}"
        shell:
          bash {0}

      - name: Set BiocVersion
        run: |
          BiocManager::install(version = "${{ matrix.config.bioc }}", ask = FALSE, update = FALSE)
        shell: Rscript {0}

      - name: Install dependencies
        run: |
          install.packages(c("remotes"))
          # remotes::install_deps(dependencies = TRUE)
          remotes::install_cran("covr", type = "binary", dependencies = TRUE)
          ## remotes::install_deps(dependencies = TRUE)
          ## remotes::install_cran("rcmdcheck")
          ### Try installing the package dependencies in steps. First the local
          ## dependencies, then any remaining dependencies to avoid the
          ## issues described at
          ## https://stat.ethz.ch/pipermail/bioc-devel/2020-April/016675.html
          ## https://github.com/r-lib/remotes/issues/296
          ## Ideally, all dependencies should get installed in the first pass.

          ## Pass #1 at installing dependencies
          message(paste('****', Sys.time(), 'pass number 1 at installing dependencies: local dependencies ****'))
          local_deps <- remotes::local_package_deps(dependencies = TRUE)
          deps <- remotes::dev_package_deps(dependencies = TRUE, repos = BiocManager::repositories())
          # BiocManager::install(local_deps[local_deps %in% deps$package[deps$diff != 0]])
          BiocManager::install(local_deps, force = TRUE)

          ## Pass #2 at installing dependencies
          message(paste('****', Sys.time(), 'pass number 2 at installing dependencies: any remaining dependencies ****'))
          deps <- remotes::dev_package_deps(dependencies = TRUE, repos = BiocManager::repositories())
          BiocManager::install(deps$package[deps$diff != 0])

          ## For running the checks
          message(paste('****', Sys.time(), 'installing rcmdcheck and BiocCheck ****'))
          remotes::install_cran("rcmdcheck")
          BiocManager::install("BiocCheck")
        shell: Rscript {0}

      - name: Test coverage
        run: covr::codecov()
        shell: Rscript {0}